If you wanted to skip using the Special/Discount system altogether, you could use an Order Total extension to give the discount, like Category & Product-Based Fee/Discount. In there you can choose the products that the discount applies to, and what the formula for the discount is.

Keep in mind this is an Order Total extension, though. Order Totals do not affect the price shown in the cart -- only "Special" prices can do that. Order Totals are automatically activated when the criteria are met, and show up as a line item on the order. If you want to inform the customer of the possible fee or discount, you'd need to do so some other way, such as a banner or HTML module. (Or just put it in the product description.)

Feel free to take a look at the screenshots and demo site, and if you're interested let me know at www.getclearthinking.com/contact if you have any further questions.

That's fine, you can choose whatever products/categories/manufacturers you want in Category & Product-Based Fee/Discount. Just add the appropriate rule to the charge, and it will only apply to those products.